feat(backend): add PRAGMA user_version migration runner + 0001_initial
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Tyler
@@ -1,13 +1,73 @@
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"""Database migration runner.
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"""PRAGMA user_version-based migration runner.
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Stub. Task 3 replaces this with a real migration implementation
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that tracks applied migrations in a ``schema_migrations`` table.
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Each migration is a `.sql` file under `backend/src/cyclone/migrations/`
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with a leading comment of the form `-- version: N`. The runner reads
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the current `PRAGMA user_version`, sorts migrations by filename, and
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applies any whose version is greater than the current value. Each
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migration runs in its own transaction; a failure rolls back the
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version bump so the next startup retries.
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This is intentionally NOT Alembic. One operator, one machine, one
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schema-version counter.
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"""
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from __future__ import annotations
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import re
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from pathlib import Path
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import sqlalchemy as sa
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MIGRATIONS_DIR = Path(__file__).parent / "migrations"
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_VERSION_RE = re.compile(r"^--\s*version:\s*(\d+)", re.MULTILINE)
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def _migration_version(sql: str, filename: str) -> int:
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m = _VERSION_RE.search(sql)
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if not m:
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raise RuntimeError(
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f"{filename}: missing '-- version: N' header comment"
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)
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return int(m.group(1))
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def _strip_comments(sql: str) -> str:
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"""Remove `--` line comments; preserve everything else."""
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lines = []
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for line in sql.splitlines():
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stripped = line.strip()
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if stripped.startswith("--"):
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continue
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lines.append(line)
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return "\n".join(lines)
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def run(engine: sa.Engine) -> None:
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"""Apply pending migrations. No-op until Task 3."""
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"""Apply any pending migrations. Idempotent."""
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migrations_dir = MIGRATIONS_DIR
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if not migrations_dir.exists():
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return # no migrations directory yet — fresh checkout, no-op
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migration_files = sorted(migrations_dir.glob("*.sql"))
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if not migration_files:
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return
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with engine.begin() as conn:
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current = conn.exec_driver_sql("PRAGMA user_version").scalar() or 0
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for path in migration_files:
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sql = path.read_text()
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version = _migration_version(sql, path.name)
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if version <= current:
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continue
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statements_sql = _strip_comments(sql)
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statements = [s.strip() for s in statements_sql.split(";") if s.strip()]
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with engine.begin() as conn:
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for stmt in statements:
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conn.exec_driver_sql(stmt)
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conn.exec_driver_sql(f"PRAGMA user_version = {version}")
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current = version
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@@ -0,0 +1,87 @@
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-- version: 1
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-- Initial schema: 6 tables for Cyclone DB + reconciliation.
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CREATE TABLE batches (
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id TEXT PRIMARY KEY,
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kind TEXT NOT NULL,
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input_filename TEXT NOT NULL,
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parsed_at DATETIME NOT NULL,
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totals_json TEXT,
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validation_json TEXT,
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raw_result_json TEXT
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);
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CREATE INDEX ix_batches_parsed_at ON batches(parsed_at DESC);
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CREATE TABLE claims (
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id TEXT PRIMARY KEY,
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batch_id TEXT NOT NULL REFERENCES batches(id) ON DELETE CASCADE,
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patient_control_number TEXT NOT NULL,
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service_date_from DATE,
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service_date_to DATE,
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charge_amount NUMERIC(12, 2) NOT NULL DEFAULT 0,
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provider_npi TEXT,
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payer_id TEXT,
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state TEXT NOT NULL DEFAULT 'submitted',
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state_before_reversal TEXT,
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matched_remittance_id TEXT REFERENCES remittances(id),
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raw_json TEXT,
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UNIQUE (batch_id, patient_control_number)
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);
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CREATE INDEX ix_claims_state ON claims(state);
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CREATE INDEX ix_claims_patient_control_number ON claims(patient_control_number);
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CREATE INDEX ix_claims_service_date_from ON claims(service_date_from);
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CREATE TABLE remittances (
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id TEXT PRIMARY KEY,
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batch_id TEXT NOT NULL REFERENCES batches(id) ON DELETE CASCADE,
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payer_claim_control_number TEXT NOT NULL,
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claim_id TEXT REFERENCES claims(id),
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status_code TEXT NOT NULL,
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status_label TEXT,
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total_charge NUMERIC(12, 2) NOT NULL DEFAULT 0,
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total_paid NUMERIC(12, 2) NOT NULL DEFAULT 0,
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patient_responsibility NUMERIC(12, 2),
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adjustment_amount NUMERIC(12, 2) NOT NULL DEFAULT 0,
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received_at DATETIME NOT NULL,
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service_date DATE,
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is_reversal INTEGER NOT NULL DEFAULT 0,
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raw_json TEXT,
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UNIQUE (batch_id, payer_claim_control_number)
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);
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CREATE INDEX ix_remittances_claim_id ON remittances(claim_id);
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CREATE INDEX ix_remittances_payer_claim_control_number ON remittances(payer_claim_control_number);
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CREATE INDEX ix_remittances_status_code ON remittances(status_code);
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CREATE TABLE cas_adjustments (
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id INTEGER PRIMARY KEY AUTOINCREMENT,
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remittance_id TEXT NOT NULL REFERENCES remittances(id) ON DELETE CASCADE,
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group_code TEXT NOT NULL,
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reason_code TEXT NOT NULL,
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amount NUMERIC(12, 2) NOT NULL,
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quantity NUMERIC(10, 2)
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);
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CREATE INDEX ix_cas_adjustments_remittance_id ON cas_adjustments(remittance_id);
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CREATE TABLE matches (
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id INTEGER PRIMARY KEY AUTOINCREMENT,
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claim_id TEXT NOT NULL UNIQUE REFERENCES claims(id) ON DELETE CASCADE,
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remittance_id TEXT NOT NULL REFERENCES remittances(id) ON DELETE CASCADE,
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strategy TEXT NOT NULL,
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matched_at DATETIME NOT NULL,
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prior_claim_state TEXT,
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is_reversal INTEGER NOT NULL DEFAULT 0
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);
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CREATE INDEX ix_matches_remittance_id ON matches(remittance_id);
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CREATE INDEX ix_matches_matched_at ON matches(matched_at);
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CREATE TABLE activity_events (
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id INTEGER PRIMARY KEY AUTOINCREMENT,
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ts DATETIME NOT NULL,
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kind TEXT NOT NULL,
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batch_id TEXT,
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claim_id TEXT,
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remittance_id TEXT,
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payload_json TEXT
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);
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CREATE INDEX ix_activity_events_ts ON activity_events(ts DESC);
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CREATE INDEX ix_activity_events_kind ON activity_events(kind);
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@@ -0,0 +1,67 @@
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"""Tests for the PRAGMA user_version migration runner."""
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from __future__ import annotations
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from pathlib import Path
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import pytest
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import sqlalchemy as sa
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from cyclone import db_migrate
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def _fresh_engine(tmp_path: Path) -> sa.Engine:
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return sa.create_engine(f"sqlite:///{tmp_path}/m.db", future=True)
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def _user_version(engine: sa.Engine) -> int:
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with engine.connect() as c:
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return c.exec_driver_sql("PRAGMA user_version").scalar() or 0
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def test_run_on_empty_db_bumps_to_latest(tmp_path: Path, monkeypatch: pytest.MonkeyPatch) -> None:
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monkeypatch.setattr(db_migrate, "MIGRATIONS_DIR", tmp_path)
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(tmp_path / "0001_initial.sql").write_text("-- version: 1\nCREATE TABLE t (id INTEGER);\n")
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engine = _fresh_engine(tmp_path)
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db_migrate.run(engine)
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assert _user_version(engine) == 1
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with engine.connect() as c:
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rows = c.exec_driver_sql("SELECT name FROM sqlite_master WHERE type='table' AND name='t'").all()
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assert len(rows) == 1
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def test_run_is_idempotent(tmp_path: Path, monkeypatch: pytest.MonkeyPatch) -> None:
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monkeypatch.setattr(db_migrate, "MIGRATIONS_DIR", tmp_path)
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(tmp_path / "0001_initial.sql").write_text("-- version: 1\nCREATE TABLE t (id INTEGER);\n")
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engine = _fresh_engine(tmp_path)
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db_migrate.run(engine)
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db_migrate.run(engine) # second call should be a no-op
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assert _user_version(engine) == 1
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def test_run_skips_already_applied_migrations(tmp_path: Path, monkeypatch: pytest.MonkeyPatch) -> None:
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monkeypatch.setattr(db_migrate, "MIGRATIONS_DIR", tmp_path)
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(tmp_path / "0001_initial.sql").write_text("-- version: 1\nCREATE TABLE t1 (id INTEGER);\n")
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(tmp_path / "0002_add_col.sql").write_text("-- version: 2\nALTER TABLE t1 ADD COLUMN name TEXT;\n")
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engine = _fresh_engine(tmp_path)
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db_migrate.run(engine)
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assert _user_version(engine) == 2
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# Modify 0002 (a no-op for SQLite ALTER, but we want to verify the
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# runner doesn't re-run already-applied migrations).
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db_migrate.run(engine)
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assert _user_version(engine) == 2
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def test_run_raises_on_missing_version_header(tmp_path: Path, monkeypatch: pytest.MonkeyPatch) -> None:
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monkeypatch.setattr(db_migrate, "MIGRATIONS_DIR", tmp_path)
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(tmp_path / "0001_bad.sql").write_text("CREATE TABLE t (id INTEGER);\n") # no header
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engine = _fresh_engine(tmp_path)
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with pytest.raises(RuntimeError, match="missing '-- version"):
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db_migrate.run(engine)
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